On January 8, I noticed that Protein Explorer (proteinexplorer.org, PE),
when operated in Internet Explorer on Windows, no longer succeeds in
loading molecules (PDB files) from PDB identification codes. This new
problem most likely results from changes made at the RCSB PDB around the
turn of the new year.
This problem occurs only when using PE in Windows Internet Explorer. I
expect to release a new version of PE that will fix this problem soon.
Until the new version, there are two workarounds.
1. Use any PE-compatible browser other than IE. See list and sources here:
http://www.umass.edu/microbio/chime/pe_alpha/protexpl/needbrow.htm?nosorry
I particularly like FireFox 1.5, out recently. Netscape 7.2 and Mozilla
also work fine (and Netscape 4.8 in Mac OSX Classic). If Netscape 8 can run
PE, I haven't been able to figure out how.
or
2. Configure PE to use an OCA source for PDB files, e.g. Boston Univ.
instead of RCSB.
- Go to proteinexplorer.org (optionally click on the Alpha release, or go
to a downloaded copy of PE).
- At PE's FrontDoor (middle gray box near bottom), start Empty Explorer.
- In PE's message box, click on Options, Preferences.
- Click on "Change Server" at the bottom of the options list.
- In the window that opens, click the button "Record Preferred PDB Mirror".
- Under the list of OCA PCB sites, click one of the Copy links, e.g. at
USA Boston. (Do NOT select an RCSB mirror; they don't work and/or have been
discontinued.)
- Click the Record button. You should now see confirmation of your
selection in red.
- Close the "how to load a molecule" page.
- Henceforth (until you change this preference) all PDB files will come
from the location you selected. The preference setting is per-workstation
(saved as a browser cookie). If you move to a different computer or
workstation, you may have to set an OCA source preference there too.
Please contact me if you have concerns not covered above.
-Eric
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Eric Martz, Professor Emeritus, Dept Microbiology
U Mass, Amherst -- http://www.umass.edu/molvis/martz
Protein Explorer - 3D Visualization: http://proteinexplorer.org
See 3D Molecules, Install Nothing! - http://firstglance.jmol.org
Workshops: http://workshops.proteinexplorer.org
Biochem 3D Education Resources http://MolviZ.org
World Index of Molecular Visualization Resources: http://molvisindex.org
ConSurf - Find Conserved Patches in Proteins: http://consurf.tau.ac.il
Atlas of Macromolecules: http://atlas.proteinexplorer.org
PDB Lite Macromolecule Finder: http://pdblite.org
Molecular Visualization EMail List (molvis-list):
http://bioinformatics.org/mailman/listinfo/molvis-list
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